bioRxiv preprint doi: https://doi.org/10.1101/2021.04.07.438755; this version posted April 7, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Title: Cells of the human intestinal tract mapped across space and time Elmentaite R1, Kumasaka N1, King HW2, Roberts K1, Dabrowska M1, Pritchard S1, Bolt L1, Vieira SF1, Mamanova L1, Huang N1, Goh Kai’En I3, Stephenson E3, Engelbert J3, Botting RA3, Fleming A1,4, Dann E1, Lisgo SN3, Katan M7, Leonard S1, Oliver TRW1,8, Hook CE8, Nayak K10, Perrone F10, Campos LS1, Dominguez-Conde C1, Polanski K1, Van Dongen S1, Patel M1, Morgan MD5,6, Marioni JC1,5,6, Bayraktar OA1, Meyer KB1, Zilbauer M9,10,11, Uhlig H12,13,14, Clatworthy MR1,4, Mahbubani KT15, Saeb Parsy K15, Haniffa M1,3, James KR1* & Teichmann SA1,16* Affiliations: 1. Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK. 2. Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK 3. Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK. 4. Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK 5. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK. 6. Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK 7. Structural and Molecular Biology, Division of Biosciences, University College London WC1E 6BT, UK 8. Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge CB2 0QQ, United Kingdom of Great Britain and Northern Ireland. 9. Wellcome Trust – MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK 10. Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK 11. Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals Trust, Cambridge, CB2 0QQ, UK 12. Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK 13. Department of Paediatrics, University of Oxford, Oxford, OX1 2JD, UK 14. NIHR Oxford Biomedical Research Centre, Oxford, OX3 7JX, UK 15. Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK 16. Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK *Corresponding author. Email: [email protected] (KRJ), [email protected] (SAT) bioRxiv preprint doi: https://doi.org/10.1101/2021.04.07.438755; this version posted April 7, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract The cellular landscape of the human intestinal tract is dynamic throughout life, developing in utero and changing in response to functional requirements and environmental exposures. To comprehensively map cell lineages in the healthy developing, pediatric and adult human gut from ten distinct anatomical regions, as well as draining lymph nodes, we used single- cell RNA-seq and VDJ analysis of roughly one third of a million cells. This reveals the presence of BEST4+ absorptive cells throughout the human intestinal tract, demonstrating the existence of this cell type beyond the colon for the first time. Furthermore, we implicate IgG sensing as a novel function of intestinal tuft cells, and link these cells to the pathogenesis of inflammatory bowel disease. We define novel glial and neuronal cell populations in the developing enteric nervous system, and predict cell-type specific expression of Hirschsprung’s disease-associated genes. Finally, using a systems approach, we identify key cell players across multiple cell lineages driving secondary lymphoid tissue formation in early human development. We show that these programs are adopted in inflammatory bowel disease to recruit and retain immune cells at the site of inflammation. These data provide an unprecedented catalogue of intestinal cells, and new insights into cellular programs in development, homeostasis and disease. Introduction Intestinal tract physiology relies on the integrated contribution of epithelial, mesenchymal, endothelial, mesothelial, innate and adaptive immune, and neuronal cell lineages, whose relative abundance and cell networking fluctuate from embryonic development to adulthood. Factors contributing to these dynamics include gut function, environmental challenges and disease states that vary at different life stages. Adding further complexity is that the intestinal tract is formed of distinct anatomical regions that develop at different rates and carry out diverse roles in digestion, nutrient absorption, metabolism, and immune regulation in adulthood. Single-cell analyses of intestinal organoids from iPSCs and human primary tissue have provided a unique opportunity to study the earliest stages of gut development. Although focused mainly on epithelial cells, they have led to identification of factors driving cellular differentiation 1,2 and novel markers of rare cell types 3. Analysis of rare fetal intestinal tissues have further resolved the formation of villi-crypt structures and seeding of immune cells into the gut environment 4,5. Similarly, our understanding of the cellular landscape of the adult gut is benefiting from single-cell technologies. We have previously reported regional differences in immune cell activation in the healthy human colon linked to variability in the microbiome composition 6 and expression of ligand-receptor pairs between cell populations has been used to infer cellular communication involving enteric neuronal cells subtypes 7. Studies comparing inflammatory bowel disease (IBD) samples to healthy controls or non-inflamed tissue have allowed for the identification of a new stromal subtype that expands in disease 89, clonal expansion of tissue-resident CD8 T cells in disease 10–12 and correlation between cellular response and clinical treatment 13. While extensive work has been carried out to profile the intestinal tract at single-cell resolution, a holistic analysis of the gut through space (anatomical location) and time (lifespan) is lacking. bioRxiv preprint doi: https://doi.org/10.1101/2021.04.07.438755; this version posted April 7, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Here, we create a broad and deep single-cell census of the healthy human gut, encompassing around 350,000 cells from 11 distinct anatomical sites during embryonic and fetal development, childhood and adulthood. In doing so, we reveal new insights into the epithelial compartment: we identify the presence of BEST4+ enterocytes in both small and large intestine and throughout life, and define a role for IgG sensing by tuft cells in IBD. In the developing enteric nervous system, we identify multiple novel populations, and highlight cell communication networks with stromal cells via receptors and ligands associated with Hirschsprung’s disease. In addition, we identify key cells and signaling networks initiating lymphoid structure formation in early human development. Interestingly, the same developmental programmes are adopted to drive recruitment of immune cells during pediatric Crohn’s disease. Thus our high-resolution genomic definition of human cells and gene expression programmes across epithelial, enteric nervous system and immune compartments uncovers new insights into both rare and common diseases of the intestines. Results Integrated view of human gut throughout life To investigate cellular profiles and communication networks across the intestinal tract, we performed scRNA-seq on distinct tissue regions of the second-trimester (12-17 post- conception weeks (PCW)) fetal and adult (29-69 years) intestine and draining mesenteric lymph nodes (mLN) (Figure 1A & Supplementary Fig. 1A). In adult samples, immune (CD45+) and non-immune (CD45-) cells were separated and loaded for scRNA-seq in equivalent proportions. To represent the gut at embryonic and early postnatal life, we incorporated our previously published embryonic (6-10 PCW; small intestine, large intestine) and pediatric (4-12 years; ileal) scRNA-seq data 4. After quality control and doublet removal, the combined dataset comprised over 346,000 intestinal cells (Supplementary Fig. 1B). Leiden clustering and marker gene analysis revealed major clusters of epithelial, mesenchymal, endothelial, lymphocytes, neuronal, myeloid and erythroid cells (Fig. 1B). Fetal gut samples were enriched for mesenchymal cells and relatively high numbers of neuronal cells, with increased abundance of immune cell types from the second trimester onwards (Figure 1C & Supplementary Fig. 2A). Mesenteric lymph nodes, collected from second-trimester onwards, predominantly contained immune cells (Figure 1C & Supplementary Fig. 2A). Further sub-clustering of the cellular populations allowed for identification of 103 cell types and states with